The identification of genes underlying important quantitative trait loci is extremely challenging in complex genomes such as Brassica napus (canola, oilseed rape or rapeseed). Recent advances in next-generation sequencing (NGS) has enabled development of millions of SNPs. However, as an increasing number of genome sequences become available, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. We have examined the SNP diversity within genes, and this allelic variation is an important source of phenotypic variation. However, we have observed significant gene presence absence variation and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome and the determination and characterisation of the pangenome is a requirement to understand variation within a species. We have developed Brassica pan genomes and using these the molecular analyses of candidate resistance genes using B. napus NGS data are presented, and the difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome will be discussed.